5-116204876-A-T

Variant names:

• chr5-116204876-A-T
• rs7709377
• NM_016144.4:c.510+70698A>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_016144.4(COMMD10):​c.510+70698A>T variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: COMMD10 NM_016144.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.25
• Publications: 7 publications found

Genes affected

COMMD10 (HGNC:30201): (COMM domain containing 10) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016144.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMMD10	NM_016144.4	MANE Select	c.510+70698A>T		intron	N/A	NP_057228.1	Q9Y6G5
	COMMD10	NM_001308080.2		c.468+70698A>T		intron	N/A	NP_001295009.1	D6RJ90

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMMD10	ENST00000274458.9	TSL:1 MANE Select	c.510+70698A>T		intron	N/A	ENSP00000274458.4	Q9Y6G5
	COMMD10	ENST00000632434.1	TSL:1	c.468+70698A>T		intron	N/A	ENSP00000488332.1	D6RJ90
	COMMD10	ENST00000515539.5	TSL:3	c.468+70698A>T		intron	N/A	ENSP00000427319.1	D6RJ90

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	15
DANN	Benign	0.69
PhyloP100		5.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7709377; hg19: chr5-115540573;